Compositions for chromosome-specific staining

Methods and compositions for staining based upon nucleic acid sequence that employ nucleic acid probes are provided. Said methods produce staining patterns that can be tailored for specific cytogenetic analyses. Said probes are appropriate for in situ hybridization and stain both interphase and metaphase chromosomal material with reliable signals. The nucleic acid probes are typically of a complexity greater than 50 kb, the complexity depending upon the cytogenetic application. Methods are provided to disable the hybridization capacity of shared, high copy repetitive sequences and/or remove such sequences to provide for useful contrast. Still further methods are provided to produce chromosome-specific staining reagents which are made specific to the targeted chromosomal material, which can be one or more whole chromosomes, one or more regions on one or more chromosomes, subsets of chromosomes and/or the entire genome. Probes and test kits are provided for use in tumor cytogenetics, in the detection of disease related loci, in analysis of structural abnormalities, such as translocations, and for biological dosimetry. Further, methods and prenatal test kits are provided to stain targeted chromosomal material of fetal cells, including fetal cells obtained from maternal blood. Still further, the invention provides for automated means to detect and analyse chromosomal abnormalities.

Skip to:  ·  Claims  ·  References Cited  · Patent History  ·  Patent History

Claims

1. Nucleic acid probes for use in in situ hybridization comprising a heterogeneous mixture that contains labeled nucleic acid fragments that are substantially complementary to unique nucleic acid segments, wherein said mixture comprises blocking nucleic acid having nucleic acid fragments which are substantially complementary to repetitive segments in the labeled nucleic acid, produced by the process of:

(a) obtaining chromosome-specific DNA fragments;
(b) amplifying said chromosome-specific DNA fragments;
(c) labeling said chromosome-specific DNA fragments with a fluorescent or affinity label; and
(d) adding sufficient blocking nucleic acid to prevent substantial binding of the labeled nucleic acid sequences to repetitive nucleic acid sequences in a target DNA.

2. Nucleic acid probes according to claim 1, wherein said step (b) of amplifying said chromosome-specific DNA fragments is performed by using a PCR process.

3. Nucleic acid probes according to claim 1, wherein said probes have a combined complexity of greater than about 40 kb.

4. Nucleic acid probes according to claim 3, wherein said probes have a combined complexity of between about 40 and about 100 kb.

5. Nucleic acid probes according to claim 1, wherein said probes have a combined complexity of greater than about 50 kb.

6. Nucleic acid probes according to claim 1, wherein said chromosome-specific DNA fragments are labeled by direct attachment of a fluorochrome.

7. Nucleic acid probes according to claim 1, wherein said chromosome-specific DNA fragments are immunochemically labeled.

8. Nucleic acid probes according to claim 1, wherein said chromosome-specific DNA fragments are labeled with biotin.

9. Nucleic acid probes according to claim 1, wherein said chromosome-specific DNA fragments are labeled by direct attachment of an enzyme.

10. Nucleic acid probes according to claim 1, wherein said chromosome-specific DNA fragments are labeled by modification with N-acetoxy-N-2-acetylaminofluorene.

11. Nucleic acid probes according to claim 1, wherein said labeled nucleic acid fragments are complementary to the total genomic complement of chromosomes, fragments complementary to a single chromosome, fragments complementary to a subset of chromosomes, or fragments complementary to a subregion of a single chromosome.

12. Nucleic acid probes according to claim 11, wherein said labeled nucleic acid fragments are selected from the nucleic acid of normal human chromosomes 1 through 22, X and Y.

13. Nucleic acid probes according to claim 12, wherein said labeled nucleic acid fragments are selected from the nucleic acid of chromosome 21.

Referenced Cited
U.S. Patent Documents
4358535 November 9, 1982 Falkow et al.
4647529 March 3, 1987 Rodland et al.
4675286 June 23, 1987 Calenoff
4681840 July 21, 1987 Stephenson et al.
4683195 July 28, 1987 Mullis et al.
4683202 July 28, 1987 Mullis
4707440 November 17, 1987 Stavrianopoulos
4710465 December 1, 1987 Weissman et al.
4711955 December 8, 1987 Ward et al.
4721669 January 26, 1988 Barton
4725536 February 16, 1988 Fritsch et al.
4770992 September 13, 1988 Van den Engh et al.
4772691 September 20, 1988 Herman
4828979 May 9, 1989 Klevan et al.
4888278 December 19, 1989 Singer et al.
5085983 February 4, 1992 Scanlon
5427932 June 27, 1995 Weier et al.
5447841 September 5, 1995 Gray et al.
5472842 December 5, 1995 Stokke et al.
Foreign Patent Documents
0430402 June 1991 EPX
2019408 October 1979 GBX
2215724 September 1989 GBX
8705027 August 1987 WOX
9005789 May 1990 WOX
Other references
  • Park et al, "Amplification, Overexpression, and Rearrangement of the erbB-2 Protooncogene in Primary Human Stomach Carcinomas," Cancer Research, vol. 49, Dec. 1989, pp. 6605-6609. Pierce et al, "Analysis Of A Dispersed Repetitive DNA Sequence In Isogenic Lines of Drosophila," Chromosoma, vol. 82, 1981, pp. 471-492. Rabin, "Mapping Minimally Reiterated Genes On Diploid Chromosomes By In Situ Hybridization," thesis, Dept. of Biochemistry, Univ. Ill., 1982. Rabin et al, "Two Homoeo Box Loci Mapped In Evolutionarily Related Mouse And Human Chromosomes," Nature, vol. 314, 1985, pp. 175-178. Ried et al, "Simultaneous Visualization of Seven Different DNA Probes by In Situ Hybridizatio Using Combinatorial Fluorescence and Digital Imaging Microscopy," PNAS (USA), vol. 89, Feb. 1992, pp. 1388-1392. Ruddle, "A New Era In Mammalian Gene Mapping: Somatic Cell Genetics And Recombinant DNA Methodologies," Nature, vol. 294, 1981, pp. 115-120. Saint-Ruf et al, "Proto-Oncogene Amplification and Homogeneously Staining Regions in Human Breast Carcinomas," Genes, Chromosomes & Cancer, vol. 2, (1990), pp. 18-26. Siracusa et al, "Use of Repetitive DNA Sequences To Distinguish Mus musculus and Mus caroli Cells By in situ Hybridization," J Embryol. exp. Morph., vol. 73, 1983, pp. 163-178. Sondermeijer et al, "The Activity of Two Heat Shock Loci of Drosophila hydei In Tissue Culture Cells and Salivary Gland Cells as Analyzed by in situ Hybridization of Complementary DNA," Chromosoma, vol. 72, 1979, pp. 281-291. Steinemann, "Multiple Sex Chromosomes in Drosophila miranda: A System to Study the Degeneration of a Chromosome," Chromasoma, vol. 86, 1982, pp. 59-76. Szabo et al, "Quantitative in Situ Hybridization of Ribosomal RNA Species to Polytene Chromosomes of Drosophila melanogaster," J. Mol. Biol., vol. 115, 1977, pp. 539-563. Dennis et al, "Cytogenetics of the Parthenogenetic Grasshopper Warramaba virgo and Its Bisexual Relatives," Chromosoma, vol. 82, 1981, pp. 453-469. Dutrillaux et al, "Characterization of Chromosomal Anomalies in Human Breast Cancer," Cancer Genet. Cytogenet., vol. 49, (1990), pp. 203-217. Gerhard et al, "Localization Of a Unique Gene By Direct Hybridization in situ," PNAS, vol. 78, 1981, pp. 3755-3759. Haase et al, "Detection of Two Viral Genomes in Single Cells By Double-Label Hybridization in Situ and Color Microradioautography," Science, vol. 227, 1985, pp. 189-192. Holden et al, "Amplified Sequences from Chromosome 15, Including Centromeres, Nucleolar Organizer Regions, and Centromeric Heterochromatin, in Homogeneously Staining Regions in the Human Melanoma Cell Line MeWo," Cancer Genet. & Cytogenet., vol. 14, 1985, pp. 131-146. Houldsworth et al, "Comparative Genomic Hybridization: An Overview," Am. J. Pathology, vol. 145, No. 6, 1994, pp. 1253-1260. Kallioniemi et al, "Comparative Genomic Hybridization for Molecular Cytogenetic Analysis of Solid Tumors," Science, vol. 258, 1992, pp. 818-821. Kallioniemi et al, "Optimizing Comparative Genomic Hybridization for Analysis of DNA Sequence Copy Number Changes in Solid Tumors," Genes, Chromosomes & Cancer, vol. 10, 1994, pp. 231-243. Kallioniemi et al, "ERBB2 Amplification in Breast Cancer Analyzed by Fluorescence in situ Hybridization," PNAS USA, vol. 89, 1992, pp. 5321-5325. Krumlauf et al, "Construction and Characterization of Genomic Libraries From Specific Human Chromosomes," PNAS, vol. 79, 1982, pp. 2971-2975. Kunkel et al, "Organization and Heterogeneity of Sequences Within A Repeating Unit Of Human Y Chromosome Deoxyribonucleic Acid," Biochem., vol. 18, 1979, pp. 3343-3353. Landegent et al, "Fine Mapping Of The Huntington Disease Linked D4S10 Locus By Non-Radioactive In Situ Hybridization," Human Genetics, vol. 73, 1986, pp. 354-357. Lichter et al, "Fluorescence In Situ Hybridization with Alu and L1 Polymerase Chain Reaction Probes for Rapid Characterization of Human Chromosomes in Hybrid Cell Lines," PNAS(USA), vol. 87, Sep. 1990, pp. 6634-6638. Litt et al, "A Highly Polymorphic Locus In Human DNA Revealed By Probes From Cosmid 1-5 Maps To Chromosome 2q35.fwdarw.37," Am J Hum Genet, vol. 38, 1986, pp. 288-296. Litt et al, "A Polymorphic Locus On The Long Arm Of Chromosome 20 Defined By Two Probes From A Single Cosmid," Human Genetics, vol. 73, 1986, pp. 340-345. Malcolm et al, "Chromosomal Localization Of A Single Copy Gene By in situ Hybridization--Human .beta. Globin Genes On The Short Arm Of Chromosome 11," Ann. Hum. Genet. vol. 45, 1981, pp. 134-141. Nelson et al, "Genomic Mismatch Scanning: A New Approach To Genetic Linkage Mapping," Nature Genetics, vol. 4, 1993, pp. 11-18. Ardeshir et al, "Structure of Amplified DNA in Different Syrian Hamster Cell Lines Resistant to N-(Phosphonacetyl)-L-Aspartate," Mol. and Cell. Biology, vol. 3, No. 11, pp. 2076-2088 (Nov. 1983). Bar-Am et al, "Detection of Amplified DNA Sequences in Human Tumor Cell Lines by Fluorescence In Situ Hybridization," Genes, Chromosomes & Cancer, vol. 4, 1992, pp. 314-320. Collins and Weissman, "Directional cloning of DNA fragments at a large distance from an initial probe: A circularization method", PNAS (USA), 81:P 6812-6816 (Nov. 1984). Erikson et al, "Heterogeneity of Chromosome 22 Breakpoint in Philadelphia-positive (Ph.sup.+) Acute Lymphocytic Leukemia," PNAS, USA, vol. 83, Mar. 1986, pp. 1807-1811. Fisher et al, "Molecular Hybridization Under Conditions of High Stringency Permits Cloned DNA Segments Containing Reiterated DNA Sequences to be Assigned to Specific Chromosomal Locations," PNAS, USA, vol. 81, pp. 520-524 (Jan. 1984). Gray et al, "Flow Cytometric Detection of Chromosome Aberrations," (Abstract) Conference on Flow Cytometry in Cell Biology and Genetics, Clift Hotel, San Francisco, California, Jan. 15, 1985-Jan. 17, 1985. Grunstein et al, "Colony Hybridization: A Method for the Isolation of Cloned DNAs That Contain A Specific Gene," PNAS, USA, vol. 72, No. 10, Oct. 1975, pp. 3961-3965. Hood et al, Molecular Biology of Eucaryotic Cells, W. A. Benjamin, Inc., Menlo Park, CA, pp. 47-51 (1975). Lewin, Genes, (2nd Ed., John Wiley & Sons, Inc. 1984) pp. 298-299 and pp. 464-465. Litt et al, "A Highly Polymorphic Locus in Human DNA Revealed by Cosmid-Derived Probes," PNAS, USA, Vol. 82, pp. 6206-6210 (Sep. 1985). Lucas et al, "Rapid Translocation Analysis Using Fluorescence In Situ Hybridization: Applied to Long Term Biological Dosimetry," (UCRL 102265 Abstract), Radiation Research Meeting, New Orleans, Louisiana, Apr. 7, 1990-Apr. 12, 1990. Pinkel et al, "Cytogenetics Using Fluorescent Nucleic Acid Probes and Quantitative Microscopic Measurement," (UCRL 93269 Abstract)--Analytical Cytology X Conference, Hilton Head Resort, Hilton Head Island, S.C., Nov. 17, 1985-Nov. 22, 1985. Pinkel et al., "Rapid Quantitative Cytogenic Analysis Using Fluorescently labeled Nucleic Acid Probes," (UCRL 93553 Abstract), U.S.-Japan Joint Environmental Panel Conf., Research Triangle Park, N.C., Oct. 21, 1985-Oct. 23, 1985. Pinkel et al, "Detection of Structural and Numerical Abnormalities in Metaphase Spreads and Interphase Nuclei Using In Situ Hybridization," Cancer Genet. and Cytogenet. (UCRL 101043 Abstract 41:236 (Oct. 1989). Pinkel et al, "Detection of Translocations and Aneuploidy in Metaphase Spreads and Interphase Nuclei by In Situ Hybridization with Probes Which Stain Entire Human Chromosomes," (UCRL 101042 Abstract), 21st Oak Ridge Conference on Advanced Concepts in the Clinical Laboratory, (Apr. 13, 1989-Apr. 14, 1989). Roelofs et al, "Gene Amplification in Human Cells May Involve Interchromosomal Transposition and Persistance of the Original DNA Region," The New Biologist, vol. 4, No. 1, (Jan. 1992), pp. 75-86. Smith et al, "Distinctive Chromosomal Structures Are Found Very Early in the Amplification of CAD Genes in Syrian Hamster Cells," Cell, vol. 63, (Dec. 21, 1990), pp. 1219-1227. Straume et al, "Chromosome Translocation of Low Radiation Doses Quantified Using Fluorescent DNA Probes," (UCRL 93837 Abstract), Radiation Research Society Meeting, Las Vegas, Nevada, Apr. 12, 1986-Apr. 17, 1986. Thompson et al, Thompson & Thompson: Genetics in Medicine, 5th ed., W.B. Saunders Co., Philadelphia, PA, pp. 38-39 (1991). Trask et al, "Early Dihydrofolate Reductase Gene Amplification Events in CHO Cells Usually Occur on the Same Chromosome Arm as the Original Locus," Genes & Development, vol. 3, (1989), pp. 1913-1925. Trask et al, "Detection of DNA Sequences in Nuclei in Suspension by In Situ Hybridization and Dual Beam Flow Cytometry," (URL 93372 Abstract)--Analytical Cytology X Conference, Hilton Head Resort, Hilton Head Island, S.C., Nov. 17, 1985-Nov. 22, 1985. Weiss et al, "Organization and Evolution of the Class I Gene Family in the Major Histocompatibility Complex of the C57BL/10 Mouse," Nature, vol. 310, No. 23, pp. 650-655 (Aug. 1984). Windle et al, "A Central Role for Chromosome Breakage in Gene Amplification, Deletion Formation, and Amplicon Integration," Genes & Development, vol. 5, (1991), pp. 160-174. Arnoldus et al, "Detection of the Philadelphia Chromosome in Interphase Nuclei (With 2 Color Plates)," Cytogenet. Cell Genet., vol. 54, 1990, pp. 108-111. Bergerheim et al, "Deletion Mapping in Human Renal Cell Carcinoma," Cancer Res., vol. 49, Mar. 1989, pp. 1390-1396. Bookstein et al, "Human Retinoblastoma Susceptibility Gene: Genomic Organization and Analysis of Heterozygous Intragenic Deletion Mutants," PNAS (USA), vol. 85, Apr. 1988, pp. 2210-2214. Cohen et al, "Hereditary Renal-Cell Carcinoma Associated with a Chromosomal Translocation," N. Engl. J. Med., vol. 301, No. 11, Sep. 1979, pp. 592-595. Cremer et al, "Rapid Metaphase and Interphase Detection Radiation-Induced Chromosome Aberrations in Human Lymphocytes by Chromosomal Suppression In Situ Huybridization," Cytometry, vol. 11, 1990, pp. 110-118. Devilee et al, "Detection of Chromosome Aneuploidy in Interphase Nuclei from Human Primary Breast Tumors Using Chromosome-specific Repetitive DNA Probes," Cancer Res., vol. 48, Oct. 1988, pp. 5825-5830. Friend et al, "A Human DNA Segment with Properties of the Gene that Predisposes to Retinoblastoma and Osteosarcoma," Nature, vol. 323, Oct. 16, 1986, pp. 643-646. Gray et al, "Fluorescence Hybridization to Human Chromosome 21 Using Probes From A Charon 21 A Library," Cytometry, (Suppl. 1), 1987, Abst. 19, pg. 4. Kievits et al, "Direct Nonradioactive In Situ Hybridization of Somatic Cell Hybrid DNA to Human Lymphocyte Chromosomes," Cytometry, vol. 11, 1990, pp. 105-109. Lichter et al, "High-Resolution Mapping of Human Chromosome 11 by in Situ Hybridization with Cosmid Clones," Science, vol. 247, Jan. 5, 1990, pp. 64-69. Lichter et al, "Is Non-Isotopic in situ Hybridization Finally Coming of Age?," Nature, vol. 345, May 1990, pp. 93-94. Nederlof et al, "Detection of Chromosome Aberrations in Interphase Tumor Nuclei by Nonradioactive In Situ Hybridation," Cancer Genet. Cytogenet., vol. 42, 1989, pp. 87-98. Pinkel et al, "Fluorescence in situ Hybridization with Human Chromosome-Specific Libraries: Detection of Trisomy 21 and Translocations of Chromosome 4," PNAS (USA), vol. 85, Dec. 1988, pp. 9138-9142. Sparkes et al, "Regional Assignment of Genes for Human Esterase D and Retinoblastoma to Chromosome Band 13q14," Science, vol. 208, May 30, 1988, pp. 1042-1044. Trent et al, "Report of the Committee on Structural Chromosome Changes in Neoplasia," Cytogenet. Cell Genet., vol. 51, 1989, pp. 533-562. Angerer et al, "In Situ Hybridization to Cellular RNAs," Genetic Engineering: Principles and Methods, Setlow and Hollaender, Eds., vol. 7, pp. 43-65, Plenum Press, New York (1985). Bayer et al, "The Use of the Avidin-Biotin Complex as a Tool in Molecular Biology," Methods of Biochemical Analysis, vol. 26, pp. 1-45 (1980). Brigati et al, "Detection of Viral Genomes in Cultured Cells and Paraffin-Embedded Tissue Sections Using Biotin-Labeled Hybridization Probes," Virology, vol. 126, pp. 32-50 (1983). Broker t al, "Electron Microscopic Visualization of tRNA Genes with Ferritin-Avidin: Biotin Labels," Nucleic Acids Research, vol. 5, No. 2, pp. 363-384 (1978). Connolly et al, "Chemical Synthesis of Oligonucleotides Containing A Free Sulphydryl Group and Subsequent Attachment of Thiol Specific Probes," Nucleic Acids Research, vol. 13, No. 12, pp. 4485-4502 (1985). Fuscoe et al, "Construction of Fifteen Human Chromosome-Specific DNA Libraries from Flow-Purified Chromosomes," Cytogenetic Cell Genetics, vol. 43, pp. 79-86 (1986). Gall et al, "Nucleic Acid Hybridization in Biological Preparations," Methods in Enzymology, vol. 21, pp. 470-480 (1981). Henderson, "Cytological Hybridization to Mammalian Chromosomes," International Review of Cytology, vol. 76, pp. 1-46 (1982). Kuhlmann, Immuno Enzyme Techniques in Cytochemistry, Verlag Chemie, Weinheim, Basel (1984) (table of contents only). Lawn et al, "The Isolation and Characterization of Linked .delta.-and .beta.-Globin Genes from a Cloned Library of Human DNA," Cell, vol. 15, pp. 1157-1174 (1978). Maniatis et al, "In Vitro Packaging of Bacteriophage .lambda. DNA," Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory, pp. 256-307 (1982). Marmur, "a Procedure for the Isolation of Deoxyribonucleic Acid from Micro-organisms," J. Mol. Biol., vol. 3, pp. 208-218 (1961). Richardson et al, "Biotin and Fluorescent Labeling of RNA Using T4 RNA Ligase," Nucleic Acids Research, vol. 11, No. 18, pp. 6167-6184 (1983). Smith et al, "The Synthesis of Oligonucleotides Containing an Aliphatic Amino Group at the 5' Terminus: Synthesis of Fluorescent DNA Primers For Use In DNA Sequence Analysis," Nucleic Acids Research, vol 13, No. 7, pp. 2399-2412 (1985). Tchen et al, "Chemically Modified Nucleic Acids as Immunodetectable Probes in Hybridization Experiments," PNAS, vol. 81, pp. 3466-3470 (1984). Bauman et al, "A New Method for Fluorescence Microscopical Localization of Specific DNA Sequences by In Situ Hybridization of Fluorochrome-Labelled RNA," Exp Cell Res, vol. 128, 1980, pp. 485-490. Boyle et al, "Differential Distribution of Long and Short Interspersed Element Sequences in the Mouse Genome: Chromosome Karyotyping By Fluorescence In Situ Hybridization," PNAS (USA), vol. 87, Oct. 1990, pp. 7757-7761. Brock et al, "Quantitative in situ Hybridization Reveals Extent of Sequence Homology Between Related DNA Sequences in Drosophila melanogaster," CHROMOSOMA, vol. 83, No. 2, pp. 159-168 (1981). Bufton et al, "A Highly Polymorphic Locus On Chromosome 16q Revealed By A Probe From A Chromosome-Specific Cosmid Library," Human Genetics, vol. 74, 1986, pp. 425-431. Bufton et al, "Four Restriction Fragment Length Polymorphisms Revealed By Probes From A Single Cosmid Map To Human Chromosome 19," Am J Hum Genet, vol. 38, 1986, pp. 447-460. Burk et al, "Organization and Chromosomal Specificity of Autosomal Homologs of Human Y Chromosome Repeated DNA," Chromosoma, vol. 92, 1985, pp. 225-233. Buroker et al, "Four Restriction Fragment Length Polymorphisms Revealed By Probes From A Single Cosmid Map To Human Chromosome 12q," Human Genetics, vol. 72, 1986, pp. 86-94. Cote et al, "Quantitation of in situ Hybridization of Ribosomal Ribonucleic Acids to Human Diploid Cells," Chromosoma, vol. 80, 1980, pp. 349-367. Cremer et al, "Preparative Dual-Beam Sorting of the Human Y Chromosome and In Situ Hybridization of Cloned DNA Probes," Cytometry, vol. 5, 1984, pp. 572-579. Davies, "The Application of DNA Recombinant Technology to the Analysis of the Human Genome and Genetic Disease," Human Genetics, vol. 58, 1981, pp. 351-357. Cantor and Schimmel, Biophysical Chemistry: The Behavior of Biological Macromoles (part III, p. 1228) (Freeman 1980). Olsen et al. (1980) Biochemistry, vol. 19, pp. 2419-2428. Szabo et al, "What's New With Hybridization in situ?," TIBS, vol. 7, No. 11, Dec. 1982, pp. 425-427. Gall et al, "Formation and Detection of RNA-DNA Hybrid Molecules in Cytological Preparations," PNAS (USA), vol. 63, 1969, pp. 378-383. Buongiorno-Nardelli et al, "Autoradiographic Detection of Molecular Hybrids between rRNA and DNA in Tissue Sections," NATURE, vol. 225, Mar. 1970, pp. 946-948. John et al, "RNA-DNA Hybrids at the Cytological Level," NATURE, vol. 223, Aug. 1969, pp. 582-587. Schardin et al, "Specific Staining of Human Chromosomes in Chinese Hamster X Man Hybrid Cell Lines Demonstrates Interphase Chromosome Territories," Hum. Genet., vol. 71, 1985, pp. 281-287. Durnam et al, "Detection of Species Specific Chromosomes in Somatic Cell Hybrids," Som. Cell Molec. Genetics, vol. 11, No. 6, 1985, pp. 571-577. Manuelidis, "Individual Interphase Chromosome Domains Revealed by in situ Hybridization," Hum. Genet., vol. 71, 1985, pp. 288-293. Herzenberg et al, "Fetal Cells in the Blood of Pregnant Women: Detection and Enrichment by Fluorescence-Activated Cell Sorting," PNAS (USA), vol. 76, No. 3, Mar. 1979, pp. 1453-1455. Britten et al, "Analysis of Repeating DNA Sequences by Reassociation," Methods of Enzymology, vol. 29, 1974, pp. 363-418. Benton et al, "Screening .lambda.gt Recombinant Clones by Hybridization to Single Plaques in situ," Science, vol. 196, 1977, pp. 180-182. Landegent et al, "Chromosomal Localization of a Unique Gene by Non-Autoradiographic in situ Hybridization," Nature, vol. 317, Sep. 1985, pp. 175-177. Schmeckpeper et al, "Partial Purification and Characterization of DNA from the Human X Chromosome," PNAS (USA), vol. 76, No. 12, Dec. 1979, pp. 6625-6528. Brison et al, "General Method for Cloning Amplified DNA by Differential Screening with Genomic Probes," Molecular and Cellular Biology, vol. 2, No. 5, May 1982, pp. 578-587. Manuelidis et al, "Chromosomal and Nuclear Distribution of the HindIII 1.9-kb Human DNA Repeat Segment," Chromosoma (Berl.), vol. 91, 1984, pp. 28-38. LLNL, "Fluorescent Labeling of Human Chromosomes with Recombinant DNA Probes," Energy & Tech. Review, Jul. 1985, pp. 84-85. LLNL, "Chromosome-Specific Human Gene Libraries", Energy & Tech. Review, Jul. 1985, pp. 82-83. Fisher et al, "Adhesive and Degradative Propertis of Human Placental Cytotrophoblast Cells In Vitro," J. Cell Biol., vol. 109, No. 2, 1989, pp. 891-902. Van Dilla et al, "Construction and Availability of Human Chromosome-Specific DNA Libraries From Flow Sorted Chromosomes: Status Report," Am. J. of Human Genetics, vol. 37 (R Supplement) Jul. 1985, p. A179. Lewin, "Genetic Probes Become Ever Sharper--Rapid Detection of Multiple-Pathogen Infections, Including Major Drug-Resistance Genes, May be Possible Using a Newly Developed Technique," Science, vol. 221, No. 4616, Sep. 1983, p. 1167. Albertson, "Mapping Muscle Protein Genes by in situ Hybridization Using Biotin-Labeled Probes," EMBO J., vol. 4, No. 10, 1985, pp. 2493-2498. Albertson, "Localization of the Ribosomal Genes in Caenorhabditis elegans Chromosomes by in situ Hybridization Using Biotin-Labeled Probes," EMBO J., vol. 3, No. 6, 1984, pp. 1227-1234. Cox et al, "Detection of mRNAs in Sea Urchin Embryos by in Situ Hybridization Using Asymmetric RNA Probes," Developmental Biology, vol. 101, 1984, pp. 485-502. Sealey, et al, "Removal of Repeated Sequences from Hybridisation Probes," Nucleic Acid Research, vol. 13, No. 6, 1985, pp. 1905-1922. Harper et al, "Localization of Single Copy DNA Sequences on G-Banded Human Chromosomes by in situ Hybridization," Chromosoma (Berl.), vol. 83, 1981, pp. 431-439. Wallace et al, "The Use of Synthetic Oligonucleotides as Hybridization Probes--II Hybridization of Oligonucleotides of Mixed Sequence to Rabbit .beta. globin DNA," Nucleic Acids Research, vol. 9, No. 4, 1981, pp. 879-894. Scalenghe et al, "Microdissection ad Cloning of DNA from a Specific Region of Drosophila melanogaster Polytene Chromosomes," Chromosoma (Berl.), vol. 82, 1981, pp. 205-216. Jabs et al, "Characterization of a Cloned DNA Sequence that is Present at Centromeres of All Human Autosomes and the X Chromosome and Shows Polymorphic Variation," PNAS (USA), vol. 81, Aug. 1984, pp. 4884-4888. Stewart et al, "Cloned DNA Probes Regionally Mapped to Human Chromosome 21 and Their Use in Determining the Origin of Nondisjunction," Nucleic Acids Research, vol. 13, No. 11, 1985, pp. 4125-4132. Landegent et al, "2-Acetylaminofluorene-Modified Probes for the Indirect Hybridocytochemical Detection of Specific Nucleic Acid Sequences," Exp. Cell Res., vol. 153, 1984, pp. 61-72. Cannizzaro et al, "In Situ Hybridization and Translocation Breakpoint Mapping II. Two Unusual t(21;22) Translocations," Cytogenet. Cell Genet., vol. 39, 1985, pp. 173-178. Kao et al, "Assignment of the Structural Gene Coding for Albumin to Human Chromosome 4," Human Genetics, vol. 62, 1982, pp. 337-341. Harper et al, "Localization of the Human Insulin Gene to the Distal End of the Short Arm of Chromosome 11," PNAS (USA), vol. 78, No. 7, Jul. 1981, pp. 4458-4460. Willard et al, "Isolation and Characterization of a Major Tandem Repeat Family from the Human X Chromosome," Nucleic Acids Research, vol. 11, No. 7, 1983, pp. 2017-2033. Manuelidis, "Different Central Nervous System Cell Types Display Distinct and Nonrandom Arrangements of Satellite DNA Sequences," PNAS (USA), vol. 81, May 1984, pp. 3123-3127. Rappold et al, "Sex Chromosome Positions in Human Interphase Nuclei as Studied by in situ Hybridization with Chromosome Specific DNA Probes," Human Genetics, vol. 67, 1984, pp. 317-322. Trask et al, "The Proximity of DNA Sequences in Interphase Cell Nuclei Is Correlated to Genomic Distance and Permits Ordering of Cosmids Spaning 250 Kilobase Pairs," Genomics, vol. 5, 1989, pp. 710-717. Pinkel et al, "Cytogenetic Analysis Using Quantitative, High-Sensitivity, Fluorescence Hybridization," PNAS (USA), vol. 83, May 1986, pp. 2934-2938. McCormick, "The Polymerase Chain Reaction and Cancer Diagnosis," Cancer Cells, vol. 1, No. 2, Oct. 1989, pp. 56-61. Lawrence et al, "Sensitive, High-Resolution Chromatin and Chromosome Mapping In Situ: Presence and Orientation of Two Closely Integrated Copies of EBV in a Lymphoma Line," Cell, vol. 52, Jan. 1988, pp. 51-61. Cremer et al, "Detection of Chromosome Aberrations in Metaphase and Interphase Tumor Cells by in situ Hybridization Using Chromosome-Specific Library Probes," Human Genetics, vol. 80, 1988, pp. 235-246. Pinkel et al, "Detection of Structural Chromosome Aberrations in Metaphase Spreads and Interphase Nuclei by in situ Hybridization High Complexity Probes Which Stain Entire Human Chromosomes," Am. J. Hum. Genet. (Supplement) vol. 43, No. 3, Sep. 1988, p. A118 (Abstract 0471: 11.5). Lichter et al, "Delineation of Individual Human Chromosomes in Metaphase and Interphase Cells by in situ Suppression Hybridization Using Recombinant DNA Libraries," Human Genet., vol. 80, 1988, pp. 224-234. Langer-Safer et al, "Immunological Method for Mapping Genes on Drosophila Polytene Chromosomes," PNAS (USA), vol. 79, 1982, pp. 4381-4385. LeGrys et al, "Clinical Applications of DNA Probes in the Diagnosis of Genetic Diseases," CRC Crit. Rev. Clin. Lab. Sci., vol. 25, No. 4, 1987, pp. 255-274. Lichter et al, "Rapid Detection of Human Chromosome 21 Aberrations by in situ Hybridization," PNAS USA, vol. 85, Dec. 1988, pp. 9664-9668. Montgomery et al, "Specific DNA Sequence Amplification in Human Neuroblastoma Cells," PNAS USA, vol. 80, Sep. 1983, pp. 5724-5728. Pinkel et al, "Cytogenetic Analysis by In Situ Hybridization with Fluorescently Labeled Nucleic Acid Probes," Cold Spring Harbor Symposia on Quantitative Biology, vol. Li, 1986, pp. 151-157. Pinkel et al, "Genetic Analysis by Quantitative Microscopy and Flow Cytometry Using Fluorescence In Situ Hybridization with Chromosome-Specific Nucleic Acid Probes," Am. J. Hum. Genet. (Supplement), vol. 39, No. 3, Sep. 1986, p. A129 (379). Pinkel et al, "Cytogenetic Analysis During Leukemia Therapy Using Fluorescence in situ Hybridization with Chromosome-specific Nucleic Acid Probes," Am. J. Hum. Genet, (Supplement), vol. 41, No. 3, Sep. 1987, p. A34 (096; 12.12). Pinkel et al, "Simplified Cytogenetics Using Biotin labeled Nucleic Acid Probes and Quantitative Fluorescence Microscopy," Am. J. Hum. Genet. (Supplement), vol. 37, No. 4, Jul. 1985, pp. A112 (328; 17.2). Cremer et al, "Detection of Chromosome Aberrations in the Human Interphase Nucleus by Visualization of Specific Target DNAs with Radioactive and Non-Radioactive in situ Hybridization Techniques: Diagnosis of Trisomy 18 with Probe L1.84," Hum. Genet., vol. 74, 1986, pp. 346-352. Cremer et al, "Rapid Interphase and Metaphase Assessment of Specific Chromosomal Changes in Neuroectodermal Tumor Cells by in Situ Hybridization with Chemically Modified DNA Probes," Exp. Cell Res., vol. 176, 1988, pp. 199-220. Selypes et al, "A Noninvasive Method for Determination of the Sex and Karyotype of the Fetus from the Maternal Blood," Hum. Genet., vol. 79, 1988, pp. 357-359. Yunis et al, "Localization of Sequences Specifying Messenger RNA to Light-Staining G-Bands of Human Chromosomes," Chromosoma (Berl.), vol. 61, 1977, pp. 335-344. Fuscoe et al, "An Efficient Method for Selecting Unique-Sequence Clones from DNA Libraries and Its Application To Fluorescent Staining of Human Chromosome 21 Using in Situ Hybridization," Genomics, vol. 5, 1989, pp. 100-109. Landegren et al, "DNA Diagnostics--Molecular Techniques and Automation," Science, vol. 242, Oct. 1988, pp. 229-237. Landegent et al, "Use of Whole Cosmid Cloned Genomic Sequences for Chromosomal Localization of Non-Radioactive in situ Hybridization," Hum. Genet., vol. 77, 1987, pp. 366-370.
Patent History
Patent number: 5756696
Type: Grant
Filed: Dec 23, 1994
Date of Patent: May 26, 1998
Assignee: Regents Of The University Of California (Oakland, CA)
Inventors: Joe W. Gray (Livermore, CA), Daniel Pinkel (Walnut Creek, CA)
Primary Examiner: Ardin H. Marschel
Law Firm: Burns, Doane, Swecker and Mathis L.L.P.
Application Number: 8/364,400
Classifications
Current U.S. Class: 536/231; 435/6; Biospecific Ligand Binding Assay (436/501); 536/241; 536/243; 536/2431; 536/2432; 536/2433; 935/77; 935/78
International Classification: C12Q 168; C07H 2102; C07H 2104;